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Homo sapiens
10 Downloadable Samples
Description
TIA1 and TIAL1 encode a family of U-rich-sequence-specific mRNA-binding proteins (mRBPs) ubiquitously expressed and conserved in metazoans. By PAR-CLIP, we determined that both proteins bind target sites with identical specificity in 3' UTRs as well as within introns proximal to 5' and 3' splice sites. Double knockout (DKO) of TIA1 and TIAL1 increased target mRNA abundance proportional to the number of binding sites and impacted the accumulation of aberrantly spliced mRNAs including the dsRNA-binding protein PRKRA, whose expression was completely blocked and subsequently triggered the activation of the dsRNA-activated protein kinase EIF2AK2/PKR and stress granule formation. Ectopic expression of PRKRA cDNA or knockout of EIF2AK2 in DKO cells rescued this phenotype. Perturbation of maturation and/or stability of additional targets also compromised cell cycle progression. Our study reveals the essential role of a single mRBP family contributing to fidelity of mRNA maturation, translation and RNA stress sensing pathways in human cells.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
This project aims to delineate the circular RNA complement of mouse brain at age 8-9 weeks
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 16 Downloadable Samples
- NextSeq 500
Description
To Identify new factors of GR-mediated mRNA decay.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 3000
Description
ADARs are RNA editing enzymes that catalyze the deamination of adenosine to inosine in double-stranded RNAs. In mammals, there are two isoforms of ADAR1 including a p110 isoform, which is constitutively and ubiquitously expressed, and a p150 isoform regulated by an IFN-inducible promoter. The mutation in ADAR1 gene causes Aicardi-Goutieres syndrome (AGS), a severe autoimmune disease in human. Furthermore, the significant decrease in RNA-editing activity was found in the p150 isoform mutant associated with AGS. In this study, we will perform transcriptome-wide analysis and identify the targets of ADAR1p150 isoform.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
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SRP023133- Gallus gallus
- 2 Downloadable Samples
- Illumina HiScanSQ, Illumina HiSeq 2000
Description
Transcriptome sequencing was performed for the chicken B-lymphoma DT40 cell line. rRNA-depletion of total RNA was done, a standard Illumina pair-end library was prepared and sequenced on Illumina HiSeq2000 and HiScan2000.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
View Samples- Saccharomyces cerevisiae
- 8 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
In Saccharomyces cerevisiae, the maturation of both pre-rRNA and pre-small nucleolar RNAs (pre-snoRNAs) involves common factors, thereby providing a potential mechanism for the coregulation of snoRNA and rRNA synthesis. In this study, we examined the global impact of the double-stranded-RNA-specific RNase Rnt1p, which is required for pre-rRNA processing, on the maturation of all known snoRNAs. In silico searches for Rnt1p cleavage signals, and genome-wide analysis of the Rnt1p-dependent expression profile, identified seven new Rnt1p substrates. Interestingly, two of the newly identified Rnt1p-dependent snoRNAs, snR39 and snR59, are located in the introns of the ribosomal protein genes RPL7A and RPL7B. In vitro and in vivo experiments indicated that snR39 is normally processed from the lariat of RPL7A, suggesting that the expressions of RPL7A and snR39 are linked. In contrast, snR59 is produced by a direct cleavage of the RPL7B pre-mRNA, indicating that a single pre-mRNA transcript cannot be spliced to produce a mature RPL7B mRNA and processed by Rnt1p to produce a mature snR59 simultaneously. The results presented here reveal a new role of yeast RNase III in the processing of intron-encoded snoRNAs that permits independent regulation of the host mRNA and its associated snoRNA.
Publication Title
Genome-wide prediction and analysis of yeast RNase III-dependent snoRNA processing signals.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 54 Downloadable Samples
Description
AML patient samples and a few normal blood sample were assayed for H3K27ac ChIP-seq and RNA-seq. We discovered subtypes of AML based on these enhancer landscapes.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 26 Downloadable Samples
- Illumina HiSeq 2500
Description
LITE-Seq 3'' end capture and sequencing of the C. elegans germline
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This microarray experiment serves to identify the genes in the Arabidopsis genome that are regulated by carbon and light signaling interactions in 7 day dark grown seedlings. The expression profile of wild-type will be compared to the cli186 mutant, a mutant defective in carbon and light signaling. Plants of both the wild-type and cli186 genotypes are treated with the following light (L) and carbon (C) treatments: -C-L, +C-L, +C+L, -C+L. Comparison of the expression profiles under all treatments will help to identify genes that are misregulated in carbon and/or light treatments in the cli186 mutant.
Publication Title
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis.
Sample Metadata Fields
Age
View Samples- Danio rerio
- 12 Downloadable Samples
- IlluminaHiSeq2500
Description
Heart tissue was enriched from 48hpf zebrafish larvae from different experimental conditions. Approximately 200 hearts were collected for each sample. The goals of the study were to profile transcriptional outputs in the cardiac tissue which affects heart development between two different experimental conditions.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
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